Seed Server is a Web application designed to provide putative orthologs to seed sequences. The major advantage of Seed Server is to circumvent the requirement of complete genomes to group putative orthologs. Its major advantage is based on UniProt entries which have associated literature such as SwissProt curated proteins. This task relies on three basics: (i) use of Seed Linkage software that clusters cognate proteins among distinct proteomes derived from multiple links to a single seed sequence; (ii) assignment to a Kegg Orthology group enriched with UniRef50 members and subsequent recruitment of the conveyed orthologs; (iii) creation of supervised PSSM matrices using the clustered proteins aiming recruitment validation. Additional filtering includes clade selection and evaluation of secondary structure overlap through seed and recruited sequences alignments.
Seeds
(UniProt_AC Ex: Q38946)
Seeds list (One per line)
SeedLinkage parameter R
SeedLinkage parameter C
SeedLinkage parameter S
SeedLinkage parameter L
PSI-BLAST self-score cutoff
